Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
4.2 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.54, Jaccard 0.37
Reason: 9 internal clashes
9 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (4.2 kcal/mol)
✓ Excellent LE (-0.961 kcal/mol/HA)
✓ Good fit quality (FQ -8.20)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (93%)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-20.177
kcal/mol
LE
-0.961
kcal/mol/HA
Fit Quality
-8.20
FQ (Leeson)
HAC
21
heavy atoms
MW
273
Da
LogP
3.82
cLogP
Final rank
1.2214
rank score
Inter norm
-0.980
normalised
Contacts
13
H-bonds 2
Interaction summary
HBD 1
HY 6
PI 3
CLASH 0
Interaction summary
HBD 1
HY 6
PI 3
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | 6RB5 | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASP116
GLU18
GLY112
ILE106
LEU17
MET113
SER109
THR117
THR335
TRP21
TYR110
VAL53
VAL58
| ||
| Current overlap | 7 | Native recall | 0.54 |
| Jaccard | 0.37 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
493 residues
| Protein target | T18 | Atoms | 7550 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 292 | 1.221420067123301 | -0.979973 | -20.1775 | 2 | 13 | 7 | 0.54 | - | - | no | Current |
| 264 | 1.2795201331883586 | -1.2555 | -26.0093 | 2 | 11 | 0 | 0.00 | - | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.177kcal/mol
Ligand efficiency (LE)
-0.9608kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.196
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
273.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.82
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
4.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
54.07kcal/mol
Minimised FF energy
49.91kcal/mol
SASA & burial
✓ computed
SASA (unbound)
511.9Ų
Total solvent-accessible surface area of free ligand
BSA total
390.1Ų
Buried surface area upon binding
BSA apolar
362.8Ų
Hydrophobic contacts buried
BSA polar
27.4Ų
Polar contacts buried
Fraction buried
76.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
93.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3075.1Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1472.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)